Philympics 2021: Prophage Predictions Perplex Programs

Roach, Michael J.; McNair, Katelyn; Giles, Sarah K; Inglis, Laura K; Pargin, Evan; Roux, Simon; Decewicz, Przemysław; Edwards, Robert A.

doi:10.1101/2021.06.03.446868

Cited by 7 publications

(8 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We show that the gut microbiota of this healthy individual contains numerous active prophages (Figure 1B), similar to what was observed in the gut of healthy mice [26]. We leveraged multiple prophage predictors [66] and focused on medium-to-high quality bacterial bins, as well as prophages found on bacterial scaffolds without host-flanking regions [26]. Prophages from scaffolds without host-flanking regions decrease accuracy of prophage assignment to host [58], but was a necessary approach as few prophages were assembled with host flanking regions.…”

Section: Discussionsupporting

confidence: 65%

Bacteriophages Playing Nice: Lysogenic bacteriophage replication stable in the human gut microbiota

Sutcliffe

Reyes²,

Maurice

2022

Preprint

View full text Add to dashboard Cite

The human gut is a dense microbial community, of which bacteria and bacteriophages are the majority. Bacteriophages, viruses of bacteria, exist stably, without major fluctuations in the gut of healthy individuals. This stability appears to be due to an absence of "kill-the-winner" dynamics, and the existence of "piggy- back-the-winner" dynamics, where lysogenic replication rather than lytic replication occurs. Revisiting the deep-viral sequencing data of a healthy individual studied over 2.4 years, we were able to improve our understanding of how these dynamics occur in healthy individuals. We assembled prophages from bacterial metagenomic data and show that these prophages were continually switching from lysogenic to lytic replication. Prophages were the source of a stable extracellular phage population continually present in low abundance, in comparison to the lytic- phage population, where taxonomic diversity diverged over 2.4 years. The switch to lytic replication, or prophage induction, appears to occur mostly through spontaneous prophage induction. The observed phage dynamics of regular spontaneous induction are ecologically important as they allow prophages to maintain their ability to replicate, avoiding degradation and their loss from the gut microbiota.

show abstract

Section: Discussionsupporting

confidence: 65%

Bacteriophages Playing Nice: Lysogenic bacteriophage replication stable in the human gut microbiota

Sutcliffe

Reyes²,

Maurice

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…In this study, we used prediction tools that search for viruses. However, because VirSorter2 has been reported to have difficulty distinguishing plasmids from viral sequences ( 51 , 56 , 57 ), we wanted to address the possibility that predictions from any tool may resemble other types of Neisseria MGEs.…”

Section: Resultsmentioning

confidence: 99%

“…PhiSpy ( 50 ) uses machine learning to search for characteristics that are unique to prophages (i.e., phages integrated in bacterial genomes), while VirSorter2 ( 51 , 88 ) combines alignment and machine learning-based approaches to identify microbial viruses. PhiSpy and VirSorter2 both performed well when evaluated for their ability to predict prophages in bacterial genomes ( 56 ). We also selected Seeker ( 52 ), which uses deep learning to detect phages without relying on sequence features (e.g., genes or k-mers) to explore potential novel prophage diversity.…”

Section: Methodsmentioning

confidence: 99%

Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species

2022

View full text Add to dashboard Cite

show abstract

“…Additionally, our inference of additional host species is limited by whether genomes encode CRISPR spacers (e.g., N. gonorrhoeae genomes do not encode CRISPR arrays). Moreover, we only used 3 virus prediction tools and among them only PhiSpy was specifically designed to predict prophages (52).…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we used prediction tools that search for viruses. However, because VirSorter2 has been reported to have difficulty distinguishing plasmids from viral sequences (49,52,53), we wanted to address the possibility that predictions from any of the tools may resemble other types of Neisseria MGEs. Specifically, we compared our predictions to known Neisseria plasmids and the Gonococcal Genetic Island (GGI).…”

Section: Few Predictions Are Similar To Neisseria Plasmids and The Go...mentioning

confidence: 99%

Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species

Orazi

Collins

Whitaker

2021

Preprint

View full text Add to dashboard Cite

The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one other, primarily via transformation and homologous recombination, and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from other prophages and MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus.IMPORTANCEDrug-resistant N. gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus, and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) have been identified and characterized in Neisseria species. In this study, we identified a large number of candidate phages integrated within the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.

show abstract

Philympics 2021: Prophage Predictions Perplex Programs

Cited by 7 publications

References 41 publications

Bacteriophages Playing Nice: Lysogenic bacteriophage replication stable in the human gut microbiota

Bacteriophages Playing Nice: Lysogenic bacteriophage replication stable in the human gut microbiota

Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species

Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species

Contact Info

Product

Resources

About